Environmental DNA

Our eDNA team use specialist genetic tools to detect natives and invaders.

Traditional methods of species monitoring can be expensive and challenging. However researchers at the Institute for Applied Ecology (IAE) have developed sensitive and cost-effective methods to confirm if a species is present in an area. This method uses traces of DNA that species

leave behind in the environment, e.g. scats, tissues and freshwater samples, and is called Environmental DNA or eDNA. Applications include detection of invaders, or rare species of conservation concern. Our team are experts in sample collection, processing and analysis.

What we do

Develop eDNA assays for the detection of a single target species and validate it both in the laboratory and the field

Multi-species detection using eDNA meta-barcoding that enables an inventory of biodiversity present in a water sample

Detection of terrestrial species from eDNA samples derived from water sources, such as feral pigs, horses, wild dogs

Our Facilities

eDNA sampling equipment and specialist water filtering facilities

Trace DNA laboratory for handling eDNA samples

Separate pre and post PCR facilities for QA/QC protocols

Sample preparation in accredited PC2 laboratories

Reference DNA and tissue databases

Animal holding facility, including freshwater and terrestrial

Our Partners

The University of Canberra host the Centre for Invasive Species Solutions and partner with them in the development of technologies to support eDNA advancements. We are also a key collaborator with the CSIRO on the Future Science Platform ‘Environomics’.

Development of a detection probability framework

Environmental DNA (eDNA) is increasingly used as a survey tool to infer species distributions. eDNA has advantages over traditional detection tools as it is non-invasive, samples are often easy to collect, and it reduces the need for taxonomic expertise. The technique does, however, require careful evaluation of sensitivity.

Researchers at the IAE have developed a framework to estimate the sensitivity of both the field and laboratory components of this method, and combine them to estimate overall sensitivity. This framework can be applied to species-specific eDNA surveys to estimate the sensitivity, or probability of detection, for three invasive aquatic species in Australia; redfin perch (Perca fluviatilis), carp (Cyprinus carpio), and Oriental weatherloach (Misgurnus anguillicaudatus).

To utilise eDNA as a management tool, the sensitivity of eDNA detection surveys has to be estimated and accounted for. This framework enables researchers to quantify overall sensitivity of a particular eDNA survey method, and to optimise sampling regimes. This ultimately provides the most robust data to inform management actions.

Photo Credit: Elise Furlan

Invasive species management

Once an invasive species becomes established, containment can provide an effective management option. This only works, however, if distribution limits are accurately detected.

Improved sensitivity of eDNA-based surveys makes this method particularly useful to determine outer distribution limits. Researchers at the IAE compared conventional monitoring methods and eDNA-based monitoring to determine the spread of the invasive redfin perch (Perca fluviatilis) in an intermittent river system. This voracious predatory fish is responsible for the continued decline of several threatened and vulnerable species in Australia, and in this system was a potential threat to the native and threatened Southern pygmy perch (Nannoperca australis). They demonstrated that eDNA was more sensitive than traditional methods and the combination of conventional and eDNA-based monitoring vastly improved redfin perch distribution data resulting in the optimal location for the construction of an exclusion barrier. This is one of the first eDNA studies to demonstrate a clear management outcome.

Photo Credit: Jonas Bylemans

Detection of spawning in threatened species

The application of eDNA for detecting reproductive activity in aquatic organisms has the potential to increase our knowledge of reproductive biology in elusive species. It also helps evaluate management actions aimed at increasing the reproductive output of endangered populations.

IAE researchers have detected spawning of a threatened freshwater fish species, Macquarie perch, by comparing the abundance of different types of eDNA produced during the spawning period. Previously, the detection of spawning in this species has been carried out using labour intensive egg-netting methods that have the potential to miss these sporadic events. This eDNA method can help evaluate whether population declines are caused either by spawning failure or high mortality rates of the early life history stages.